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2h2m

Solution Structure of the N-terminal domain of COMMD1 (Murr1)

Method: SOLUTION NMR Dmax: 52.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

COMM domain-containing protein 1

Homo sapiens

UniProt Q8N668

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–108 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.1；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition：0.6mM N-COMMD1, U-15N,13C 25mM phosphate buffer, 50mM NaCl, pH 6.1, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.95mM N-COMMD1, U-15N,13C 25mM phosphate buffer, 50mM NaCl, pH 6.1, 100% D2O | 100% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2H2M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8F2R Human CCC complex Deposited 2022-11-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–187（187 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8F2U Human CCC complex Deposited 2022-11-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–190（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；50 mM HEPES pH7.2, 150 mM NaCl, 2mM beta-mercaptoethanol, 0.01% Triton-X100
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
8P0W Structure of the human Commander complex COMMD ring Deposited 2023-05-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–190（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COMD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 1–108

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2h2m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2h2m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2h2m
Deposition date deposition_date2006-05-19
Structure title titleSolution Structure of the N-terminal domain of COMMD1 (Murr1)
Keywords keywordsall alpha-helical, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.43 Å
Radius of gyration Rg (electron density) rg_electron13.98 Å
Forward intensity I(0) i0748138000.00
Molecular weight molecular_weight237540.0 kDa
Excluded volume excluded_volume299800 ų
Envelope volume envelope_volume32297 ų
Hydration-shell volume shell_volume16270 ų
Envelope diameter envelope_diameter58.0 Å
Shell Rg shell_rg22.84 Å
Envelope Rg envelope_rg17.07 Å
Shape Rg shape_rg13.98 Å
Total Rg total_rg14.20 Å
Total atoms total_atoms33694
Residues n_residues2160
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax52.0 Å
Rg (real space) rg_real14.36 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real7.4810e+08
I(0) uncertainty (real space) i0_real_error9.1650e+06
Rg (reciprocal space) rg_reciprocal14.37 Å
I(0) (reciprocal space) i0_reciprocal748100000.0000
Solution quality estimate total_estimate0.8370
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.1 Å
Skewness Skewness skewness0.152
Kurtosis Kurtosis kurtosis-0.274
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha288300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.635; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)